Method getLine

src/fastqreader.cpp:240–307

}

void FastqReader::getLine(string* line){
	int copied = 0;

	int start = mBufUsedLen;
	int end = start;

	while(end < mBufDataLen) {
		if(mFastqBuf[end] != '\r' && mFastqBuf[end] != '\n')
			end++;
		else
			break;
	}

	// this line well contained in this buf, or this is the last buf
	if(end < mBufDataLen || bufferFinished()) {
		int len = end - start;
		line->assign(mFastqBuf+start, len);

		// skip \n or \r
		end++;
		// handle \r\n
		if(end < mBufDataLen-1 && mFastqBuf[end-1]=='\r' && mFastqBuf[end] == '\n')
			end++;

		mBufUsedLen = end;

		return ;
	}

	// this line is not contained in this buf, we need to read new buf
	line->assign(mFastqBuf+start, mBufDataLen - start);

	while(true) {
		readToBuf();
		start = 0;
		end = 0;
		// handle the case that \r or \n in the start of buf
		if(line->empty()) {
			while(start < mBufDataLen && (mFastqBuf[start] == '\r' || mFastqBuf[start] == '\n'))
				start++;
			end = start;
		}
		while(end < mBufDataLen) {
			if(mFastqBuf[end] != '\r' && mFastqBuf[end] != '\n')
				end++;
			else
				break;
		}
		// this line well contained in this buf
		if(end < mBufDataLen || bufferFinished()) {
			int len = end - start;
			line->append(mFastqBuf+start, len);

			// skip \n or \r
			end++;
			// handle \r\n
			if(end < mBufDataLen-1 && mFastqBuf[end] == '\n')
				end++;